Being on the train has the sense of being aboard or being a passenger on a conveyance.

Being in the train has the sense of being a component member of the train. Keep in mind that the word train refers to more than just railroads, and that a railroad train is something that comprises a group of connected cars and locomotive engines. It is proper to say that the car you are riding in is in the train. You would be in the train if you were part of a walking tour group or pilgrimage -- or even caught up in a conga line.

You are in carriage D, and carriage D is in the train. The train is the group of cars, etc., that forms a line. You are not a part of the line, so you cannot be in the train; you are merely riding in one of the cars that is part of the line.
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byeFeb 26 '11 at 22:45

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That appears to make it more logical. However, I've got off the train and now I'm on the bus.
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onestopFeb 26 '11 at 22:58

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Old usage -- omnibus carriages (the current version is just a motorized version of something that has been around for centuries) have not always been enclosed (and some still are not). Keep throwing -- I'll keep catching :o).
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byeFeb 27 '11 at 1:04

There's probably no rhyme or reason to prepositions in most languages: they're shifty creatures. Russians work ON a factory, Spanish people lie IN a beach and the French use 'de' or 'a' for nearly everything.
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David GarnerFeb 9 at 20:49

You're on because you got on. Like you're in the shower, bath or car because you got in. Unless you're on the roof of the car.

If you are on the roof of the train, you're on [the] top of the train. When you're on the train, you can go in the buffet car, when you do, you'll be in the buffet car of the train.

You also get off the train, but get out of your car, bath or shower. Probably because you got on, possibly because it is short for getting on board.

The word train, is from the French verb traîner, to pull. So it's called a train because it's being pulled, that might explain why you need to be on the train (to be pulled), rather than in it (to be pulling).